DTDA_ARCFU
ID DTDA_ARCFU Reviewed; 278 AA.
AC O29630;
DT 06-JUN-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 25-MAY-2022, entry version 118.
DE RecName: Full=D-aminoacyl-tRNA deacylase {ECO:0000255|HAMAP-Rule:MF_00562};
DE EC=3.1.1.96 {ECO:0000255|HAMAP-Rule:MF_00562};
DE AltName: Full=D-tyrosyl-tRNA(Tyr) deacylase;
GN Name=dtdA {ECO:0000255|HAMAP-Rule:MF_00562}; OrderedLocusNames=AF_0625;
OS Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC
OS 100126 / VC-16).
OC Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae;
OC Archaeoglobus.
OX NCBI_TaxID=224325;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16;
RX PubMed=9389475; DOI=10.1038/37052;
RA Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A.,
RA Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L.,
RA Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D.,
RA Quackenbush J., Lee N.H., Sutton G.G., Gill S.R., Kirkness E.F.,
RA Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N.,
RA Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R.,
RA Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D.,
RA Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P.,
RA Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M.,
RA Smith H.O., Woese C.R., Venter J.C.;
RT "The complete genome sequence of the hyperthermophilic, sulphate-reducing
RT archaeon Archaeoglobus fulgidus.";
RL Nature 390:364-370(1997).
RN [2]
RP COFACTOR.
RX PubMed=16844682; DOI=10.1074/jbc.m605860200;
RA Ferri-Fioni M.-L., Fromant M., Bouin A.-P., Aubard C., Lazennec C.,
RA Plateau P., Blanquet S.;
RT "Identification in archaea of a novel D-Tyr-tRNATyr deacylase.";
RL J. Biol. Chem. 281:27575-27585(2006).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.83 ANGSTROMS).
RG Midwest center for structural genomics (MCSG);
RT "Crystal structure of conserved hypothetical protein AF0625.";
RL Submitted (APR-2005) to the PDB data bank.
CC -!- FUNCTION: D-aminoacyl-tRNA deacylase with broad substrate specificity.
CC By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules,
CC this enzyme counteracts the toxicity associated with the formation of
CC D-aminoacyl-tRNA entities in vivo. {ECO:0000255|HAMAP-Rule:MF_00562}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA +
CC H(+); Xref=Rhea:RHEA:13953, Rhea:RHEA-COMP:10123, Rhea:RHEA-
CC COMP:10124, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:59871,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:79333; EC=3.1.1.96;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00562};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=glycyl-tRNA(Ala) + H2O = glycine + H(+) + tRNA(Ala);
CC Xref=Rhea:RHEA:53744, Rhea:RHEA-COMP:9657, Rhea:RHEA-COMP:13640,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57305,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:78522; EC=3.1.1.96;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00562};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00562,
CC ECO:0000269|PubMed:16844682};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000255|HAMAP-Rule:MF_00562,
CC ECO:0000269|PubMed:16844682};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00562}.
CC -!- SIMILARITY: Belongs to the DtdA deacylase family. {ECO:0000255|HAMAP-
CC Rule:MF_00562}.
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DR EMBL; AE000782; AAB90614.1; -; Genomic_DNA.
DR PIR; A69328; A69328.
DR RefSeq; WP_010878129.1; NC_000917.1.
DR PDB; 1YQE; X-ray; 1.83 A; A=1-278.
DR PDBsum; 1YQE; -.
DR AlphaFoldDB; O29630; -.
DR SMR; O29630; -.
DR STRING; 224325.AF_0625; -.
DR EnsemblBacteria; AAB90614; AAB90614; AF_0625.
DR GeneID; 24794228; -.
DR KEGG; afu:AF_0625; -.
DR eggNOG; arCOG01616; Archaea.
DR HOGENOM; CLU_056464_1_0_2; -.
DR OMA; CYEATHH; -.
DR OrthoDB; 84039at2157; -.
DR PhylomeDB; O29630; -.
DR BRENDA; 3.1.1.96; 414.
DR EvolutionaryTrace; O29630; -.
DR Proteomes; UP000002199; Chromosome.
DR GO; GO:0051499; F:D-aminoacyl-tRNA deacylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019478; P:D-amino acid catabolic process; IEA:UniProtKB-UniRule.
DR HAMAP; MF_00562; Deacylase_DtdA; 1.
DR InterPro; IPR018033; Deacylase_DtdA_archaea.
DR InterPro; IPR007508; DtdA.
DR PANTHER; PTHR34667; PTHR34667; 1.
DR Pfam; PF04414; tRNA_deacylase; 1.
DR PIRSF; PIRSF016210; UCP016210; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..278
FT /note="D-aminoacyl-tRNA deacylase"
FT /id="PRO_0000158964"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 11..20
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 27..31
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 34..38
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 43..49
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 57..61
FT /evidence="ECO:0007829|PDB:1YQE"
FT TURN 62..64
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 68..77
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 84..88
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 110..121
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 122..126
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 131..134
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 148..156
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 157..160
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 163..178
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 185..190
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 197..205
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 206..214
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 216..221
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 224..234
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 237..241
FT /evidence="ECO:0007829|PDB:1YQE"
FT TURN 243..245
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 248..261
FT /evidence="ECO:0007829|PDB:1YQE"
FT STRAND 264..267
FT /evidence="ECO:0007829|PDB:1YQE"
FT HELIX 268..274
FT /evidence="ECO:0007829|PDB:1YQE"
SQ SEQUENCE 278 AA; 31458 MW; 330A65B76D9A7A34 CRC64;
MKLVVCSESD TAGQNIKDNL LTFADFEEKD VGEFKLYLSD EFYIAETKER LIYADHIDEK
LAKYIDFEEI LFASRHSSKD GRKIFTVHVS GNVGTADFGG KPYSLAKPSP QTMKNYVLAL
RERLDRKPEF EFTMEVTHHG PSEISKPSAF YEIGSTEEEW KDREAAEVVA EAMLDAIRAE
KMDWNVAVGV GGTHYAPRQT EIMLTTTFTF GHNFAKYTFE HLTAEFLVKA VKLSEAEYII
IDEKSVNSAV KKIVNEAAEV AGVEVLKSKK VKKDFRLV
